Author: plessy Date: 2008-07-31 10:51:53 +0000 (Thu, 31 Jul 2008) New Revision: 2372
Removed: trunk/packages/axparafit/trunk/debian/patches/ Modified: trunk/packages/axparafit/trunk/debian/axparafit.1 trunk/packages/axparafit/trunk/debian/changelog trunk/packages/axparafit/trunk/debian/compat trunk/packages/axparafit/trunk/debian/control trunk/packages/axparafit/trunk/debian/copyright trunk/packages/axparafit/trunk/debian/rules Log: Updating for Lenny+1. - Added myself to the uploaders. - Removed the Makefile patch. - Modified debian/rules to call make with Debian-specific values. (This was done before by the Makefile patch.) - Refreshed manpage. - Updated build-dependancies to new names of Atlas packages. - Updated to Debhelper 7. - Started to update debian/copyright, found non-free headers and stopped work for the moment. Modified: trunk/packages/axparafit/trunk/debian/axparafit.1 =================================================================== --- trunk/packages/axparafit/trunk/debian/axparafit.1 2008-07-31 10:21:43 UTC (rev 2371) +++ trunk/packages/axparafit/trunk/debian/axparafit.1 2008-07-31 10:51:53 UTC (rev 2372) @@ -11,7 +11,7 @@ .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" -axparafit, axparafitblas, axparparafit, axparparafitblas, axparparafitblas_random - optimized statistical analysis of host-parasite coevolution +axparafit, axparafitblas, axparparafit, axparparafitblas, axparparafitblas_random \- optimized statistical analysis of host-parasite coevolution .SH "SYNOPSIS" .HP 10 \fBaxparafit\fR \fB\-p\ \fR\fB\fInumberOfPermutations\fR\fR \fB\-n1\ \fR\fB\fIN1\fR\fR \fB\-n2\ \fR\fB\fIN2\fR\fR \fB\-n3\ \fR\fB\fIN3\fR\fR \fB\-n4\ \fR\fB\fIN4\fR\fR \fB\-A\ \fR\fB\fIassociationMatrix\fR\fR @@ -22,74 +22,74 @@ .br \fB\-h\fR .HP 4 -(1) [\fB\-g\fR\ is\ \fInot\ available\fR\ in\ \fBaxparparafit\fR,\ \fBaxparparafitblas\fR\ and\ \fBaxparparafitblas_random\fR\.] +(1) [\fB\-g\fR\ is\ \fInot\ available\fR\ in\ \fBaxparparafit\fR,\ \fBaxparparafitblas\fR\ and\ \fBaxparparafitblas_random\fR\&.] .sp -1n .HP 4 -(2) [\fB\-t\fR\ is\ \fIrequired\fR\ for\ \fBaxparparafit\fR,\ \fBaxparparafitblas\fR\ and\ \fBaxparparafitblas_random\fR\.] +(2) [\fB\-t\fR\ is\ \fIrequired\fR\ for\ \fBaxparparafit\fR,\ \fBaxparparafitblas\fR\ and\ \fBaxparparafitblas_random\fR\&.] .sp -1n .HP 4 -(3) [\fB\-r\fR\ is\ \fIonly\fR\ available\ for\ \fBaxparparafitblas_random\fR\.] +(3) [\fB\-r\fR\ is\ \fIonly\fR\ available\ for\ \fBaxparparafitblas_random\fR\&.] .SH "DESCRIPTION" .PP -AxParafit is a highly optimized version of Pierre Legendre\'s Parafit program for statistical analysis of host\-parasite coevolution\. AxParafit has been parallelized with MPI (Message Passing Interface) for compute clusters and was used to carry out the largest co\-evolutionary analysis to date for the paper describing the software\. +AxParafit is a highly optimized version of Pierre Legendre\'s Parafit program for statistical analysis of host\-parasite coevolution\&. AxParafit has been parallelized with MPI (Message Passing Interface) for compute clusters and was used to carry out the largest co\-evolutionary analysis to date for the paper describing the software\&. .PP -AxParafit will start executing individual tests of cospeciation directly\. If you want to execute only global tests of cospeciation, please use the +AxParafit will start executing individual tests of cospeciation directly\&. If you want to execute only global tests of cospeciation, please use the [\-g] -option\. +option\&. .SH "OPTIONS" .PP \fB\-p\fR .RS 4 -Specify the number of permutations you want to execute\. +Specify the number of permutations you want to execute\&. .RE .PP \fB\-n1 \fR\fB\fIN1\fR\fR .RS 4 Specify number of Rows in -\fIassociationMatrix\fR\. +\fIassociationMatrix\fR\&. .RE .PP \fB\-n2 \fR\fB\fIN2\fR\fR .RS 4 Specify number of Columns in -\fIassociationMatrix\fR\. +\fIassociationMatrix\fR\&. .RE .PP \fB\-n3 \fR\fB\fIN3\fR\fR .RS 4 Specify number of Rows in -\fIhostMatrix\fR\. +\fIhostMatrix\fR\&. .RE .PP \fB\-n4 \fR\fB\fIN4\fR\fR .RS 4 Specify number of Columns in -\fIparasiteMatrix\fR\. +\fIparasiteMatrix\fR\&. .RE .PP \fB\-A \fR\fB\fIassociationMatrix\fR\fR .RS 4 -Specify file name of associaton matrix\. +Specify file name of associaton matrix\&. .RE .PP \fB\-B \fR\fB\fIparasiteMatrix\fR\fR .RS 4 -Specify file name of parasite matrix\. +Specify file name of parasite matrix\&. .RE .PP \fB\-C \fR\fB\fIhostMatrix\fR\fR .RS 4 -Specify file name of host matrix\. +Specify file name of host matrix\&. .RE .PP \fB\-n \fR\fB\fIrunID\fR\fR .RS 4 -Specify a run Name/ID for this run which will be appended to the output files\. +Specify a run Name/ID for this run which will be appended to the output files\&. .RE .PP [\fB\-g\fR] .RS 4 -Execute global test of cospeciation only\. +Execute global test of cospeciation only\&. .sp This is \fInot available\fR @@ -97,12 +97,12 @@ \fBaxparparafit\fR, \fBaxparparafitblas\fR and -\fBaxparparafitblas_random\fR\. +\fBaxparparafitblas_random\fR\&. .RE .PP [\fB\-t \fR\fB\fItraceFileName\fR\fR] .RS 4 -Specify the name of a binary trace\-file written by a global cospeciation test with AxParafit\. +Specify the name of a binary trace\-file written by a global cospeciation test with AxParafit\&. .sp This argument is \fIrequired\fR @@ -110,20 +110,20 @@ \fBaxparparafit\fR, \fBaxparparafitblas\fR and -\fBaxparparafitblas_random\fR\. +\fBaxparparafitblas_random\fR\&. .RE .PP [\fB\-r \fR\fB\fInumberOfRandomLinks\fR\fR] .RS 4 Only for -\fBaxparparafitblas_random\fR: specify the number of randomly selected individual cospeciation tests\. Defaults to the number of non\-zero entries in +\fBaxparparafitblas_random\fR: specify the number of randomly selected individual cospeciation tests\&. Defaults to the number of non\-zero entries in \fIassociationMatrix\fR -(equivalent to full analysis)\. +(equivalent to full analysis)\&. .RE .PP \fB\-h\fR .RS 4 -Displays an help message\. +Displays an help message\&. .RE .SH "SEE ALSO" .PP @@ -131,21 +131,21 @@ (1) .PP The programs are documented by -Alexandros Stamatakis, Alexander Auch, Jan Meier\-Kolthoff, Markus G\(:oker: "AxPcoords & Parallel AxParafit: Statistical Co\-Phylogenetic Analyses on Thousands of Taxa", BMC Bioinformatics 8:405, 2007\. +Alexandros Stamatakis, Alexander Auch, Jan Meier\-Kolthoff, Markus G\(:oker: "AxPcoords & Parallel AxParafit: Statistical Co\-Phylogenetic Analyses on Thousands of Taxa", BMC Bioinformatics 8:405, 2007\&. .PP Homepage: -http://icwww\.epfl\.ch/~stamatak/AxParafit\.html +http://icwww\&.epfl\&.ch/~stamatak/AxParafit\&.html .SH "AUTHOR" .PP This manual page was written by David Paleino -<[EMAIL PROTECTED]> +<d\&[EMAIL PROTECTED]&.com> for the Debian(TM) -system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document under the terms of the +system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU -General Public License, Version 3 any later version published by the Free Software Foundation\. +General Public License, Version 3 any later version published by the Free Software Foundation\&. .PP -On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL\. +On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL\&. .SH "COPYRIGHT" Copyright \(co 2007 Alexandros Stamatakis <[EMAIL PROTECTED]>, Alexander Auch, Jan Meier-Kolthoff, Markus G\(:oker .br Modified: trunk/packages/axparafit/trunk/debian/changelog =================================================================== --- trunk/packages/axparafit/trunk/debian/changelog 2008-07-31 10:21:43 UTC (rev 2371) +++ trunk/packages/axparafit/trunk/debian/changelog 2008-07-31 10:51:53 UTC (rev 2372) @@ -2,4 +2,4 @@ * Initial release (Closes: #463219) - -- David Paleino <[EMAIL PROTECTED]> Wed, 30 Jan 2008 11:52:11 +0100 + -- Charles Plessy <[EMAIL PROTECTED]> Thu, 31 Jul 2008 13:53:00 +0900 Modified: trunk/packages/axparafit/trunk/debian/compat =================================================================== --- trunk/packages/axparafit/trunk/debian/compat 2008-07-31 10:21:43 UTC (rev 2371) +++ trunk/packages/axparafit/trunk/debian/compat 2008-07-31 10:51:53 UTC (rev 2372) @@ -1 +1 @@ -5 +7 Modified: trunk/packages/axparafit/trunk/debian/control =================================================================== --- trunk/packages/axparafit/trunk/debian/control 2008-07-31 10:21:43 UTC (rev 2371) +++ trunk/packages/axparafit/trunk/debian/control 2008-07-31 10:51:53 UTC (rev 2372) @@ -2,10 +2,10 @@ Section: science Priority: optional Maintainer: Debian-Med Packaging Team <[EMAIL PROTECTED]> -Uploaders: David Paleino <[EMAIL PROTECTED]> -Build-Depends: debhelper (>= 5.0.0), quilt, - refblas3-dev, atlas3-base-dev, libmpich1.0-dev -Standards-Version: 3.7.3 +Uploaders: David Paleino <[EMAIL PROTECTED]>, Charles Plessy <[EMAIL PROTECTED]> +Build-Depends: debhelper (>= 7), quilt, + libblas-dev, libmpich1.0-dev +Standards-Version: 3.8.0 Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/axparafit/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/axparafit/trunk/?rev=0&sc=0 Modified: trunk/packages/axparafit/trunk/debian/copyright =================================================================== --- trunk/packages/axparafit/trunk/debian/copyright 2008-07-31 10:21:43 UTC (rev 2371) +++ trunk/packages/axparafit/trunk/debian/copyright 2008-07-31 10:51:53 UTC (rev 2372) @@ -1,23 +1,33 @@ -Source: http://icwww.epfl.ch/~stamatak/AxParafit.html +Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=226 +Upstream-Name: AxParafit +Upstream-Maintainer: Alexandros Stamatakis <[EMAIL PROTECTED]> + Alexander Auch + Jan Meier-Kolthoff + Markus Göker +Upstream-Source: http://icwww.epfl.ch/%7Estamatak/index-Dateien/countSourceAx.php -Files: debian/* -Copyright: © 2008, David Paleino <[EMAIL PROTECTED]> -License: GPL-2+ - This package is free software; you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 3 of the License, or - (at your option) any later version. - Files: * Copyright: © 2007, Alexandros Stamatakis <[EMAIL PROTECTED]> Alexander Auch Jan Meier-Kolthoff Markus Göker + +THE WEBSITE SAYS GPL BUT THE HEADERS SAY NON-COMMERCIAL. WE HAVE TO INVESTIGATE BEFORE UPLOADING. + License: GPL-2+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. -On Debian systems, the complete text of the licenses can be found in: -GPL-2 - `/usr/share/common-licenses/GPL-2' +X-Comment: On Debian systems, the complete text of the GNU GPL version 2 can be + found in: `/usr/share/common-licenses/GPL-2' + +Files: debian/* +Copyright: © 2008, David Paleino <[EMAIL PROTECTED]> +License: GPL-2+ + This package is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 3 of the License, or + (at your option) any later version. + Modified: trunk/packages/axparafit/trunk/debian/rules =================================================================== --- trunk/packages/axparafit/trunk/debian/rules 2008-07-31 10:21:43 UTC (rev 2371) +++ trunk/packages/axparafit/trunk/debian/rules 2008-07-31 10:51:53 UTC (rev 2372) @@ -6,20 +6,25 @@ include /usr/share/quilt/quilt.make +CFLAGS = -Wall -g -fomit-frame-pointer -funroll-loops +LDFLAGS = -Wl,-z,defs,--as-needed +BLAS_CFLAGS = $(CFLAGS) -D_USE_ATLAS +BLAS = -lm -lcblas -latlas + + DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE) -CFLAGS = -Wall -g -fomit-frame-pointer -funroll-loops #-D_HAND_OPTIMIZED_MM -LDFLAGS = -lm -lcblas -latlas -Wl,-z,defs,--as-needed - ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) - CFLAGS += -O0 + CFLAGS += -O0 + BLAS_CFLAGS += -O0 else - CFLAGS += -O2 + CFLAGS += -O2 + BLAS_CFLAGS += -O2 endif ifeq ($(DEB_BUILD_GNU_TYPE), x86-64-linux) - CFLAGS += -m64 + ARCH=64 else - CFLAGS += -m32 + ARCH=32 endif XP=xsltproc -o debian/ -nonet --param man.charmap.use.subset "0" @@ -33,7 +38,11 @@ build: build-stamp build-stamp: patch dh_testdir - $(MAKE) CFLAGS="$(CFLAGS) -D_HAND_OPTIMIZED_MM" BLAS_CFLAGS="$(CFLAGS) -D_USE_ATLAS" LINKERFLAGS="$(LDFLAGS)" + $(MAKE) CFLAGS="$(CFLAGS) -D_HAND_OPTIMIZED_MM" \ + BLAS_CFLAGS="$(BLAS_CFLAGS)" \ + BLAS="$(BLAS)" \ + LINKERFLAGS="$(LDFLAGS)" \ + ARCH="$(ARCH)" touch $@ clean: unpatch _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
